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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PREDICTED SUBUNIT OF TRNA METHYLTRANSFERASE FROM METHANOCALDOCOCCUS JANNASCHII DSM
 
Authors :  R. Wu, R. Zhang, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  30 Sep 09  (Deposition) - 12 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Predicted Subunit Of Trna Methyltransferase, Methanocaldococcus Jannaschii Dsm , Crystal Structure, Psi- 2, Protein Structure Initiative, Structural Genomics, Midwest Center For Structural Genomics (Mcsg) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, R. Zhang, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
The Crystal Structure Of Predicted Subunit Of Trna Methyltransferase From Methanocaldococcus Jannaschii Dsm
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0690
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PDM68
    Gene: MJ0690
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Strain: DSM 2661
    Synonym: PREDICTED SUBUNIT OF TRNA METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:11 , GLY B:13 , LYS B:14 , ASP B:15 , SER B:16 , ARG B:107BINDING SITE FOR RESIDUE GOL B 201
2AC2SOFTWARESER F:11 , GLY F:13 , ASP F:15 , SER F:16 , ARG F:107BINDING SITE FOR RESIDUE GOL F 201
3AC3SOFTWARESER C:11 , GLY C:13 , LYS C:14 , ASP C:15 , SER C:16 , ARG C:107 , HIS C:188BINDING SITE FOR RESIDUE GOL C 201
4AC4SOFTWARESER E:11 , GLY E:13 , LYS E:14 , ASP E:15 , SER E:16 , ARG E:107 , ASP E:165BINDING SITE FOR RESIDUE GOL E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K32)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Val A:112 -Pro A:113
2Val B:112 -Pro B:113
3Val C:112 -Pro C:113
4Val D:112 -Pro D:113
5Val E:112 -Pro E:113
6Val F:112 -Pro F:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K32)

(-) Exons   (0, 0)

(no "Exon" information available for 3K32)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:191
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
           Y690_METJA     3 LMDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh.eeeeeeeee......hhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eee............hhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhheeeeee.------..hhhhhhhhhhhhh.hhhhh...-.eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k32 A   3 LmDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEIK------SDYEAEIRHILKERGESPEKYFPE-KQTRVVGLKKEI 200
                             |      12        22        32        42        52        62        72|       82        92       102       112       122  |    132   |   142       152    |    - |     172       182    | |192        
                             |                                                                   73-MSE                                             125-MSE    136-MSE              157    164                    187 |           
                             4-MSE                                                                                                                                                                                  189           


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
           Y690_METJA     3 LMDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eee............hhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhheeeeee.........hhhhhhhhhhhhh.hhhhhh.--.eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k32 B   3 LmDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFP--KQTRVVGLKKEI 200
                             |      12        22        32        42        52        62        72|       82        92       102       112       122  |    132   |   142       152       162       172       182   |  |192        
                             4-MSE                                                               73-MSE                                             125-MSE    136-MSE                                           186  |           
                                                                                                                                                                                                                    189           


Chain C from PDB  Type:PROTEIN  Length:195
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
           Y690_METJA     3 LMDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eee............hhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhheeeee..---.....hhhhhhhhhhhh..hhhhh......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k32 C   3 LmDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEIK---KLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
                             |      12        22        32        42        52        62        72|       82        92       102       112       122  |    132   |   142       152    |  162       172       182       192        
                             4-MSE                                                               73-MSE                                             125-MSE    136-MSE              157 161                                       


Chain D from PDB  Type:PROTEIN  Length:191
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       
           Y690_METJA     4 MDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eee............hhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhheeeee.------...hhhhhhhhhhhhh.hhhhh......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k32 D   4 mDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEI------SSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
                            |       13        23        33        43        53        63        73        83        93       103       113       123 |     133  |    143       153  |    163       173       183       193       
                            4-MSE                                                               73-MSE                                             125-MSE    136-MSE             156    163                                     


Chain E from PDB  Type:PROTEIN  Length:191
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       
           Y690_METJA     4 MDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eee............hhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhheeeeee------...hhhhhhhhhhhhh.hhhhh.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k32 E   4 mDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEI------SSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
                            |       13        23        33        43        53        63        73        83        93       103       113       123 |     133  |    143       153  |    163       173       183       193       
                            4-MSE                                                               73-MSE                                             125-MSE    136-MSE             156    163                                     


Chain F from PDB  Type:PROTEIN  Length:193
 aligned with Y690_METJA | Q58102 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
           Y690_METJA     3 LMDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEMRKNIQYITPLMGFGYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Asn_synthase-3k32F01 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Asn_synthase-3k32F02 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) Asn_synthase-3k32F03 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) Asn_synthase-3k32F04 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) Asn_synthase-3k32F05 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) Asn_synthase-3k32F06 F:3-91                                                              ------------------------------------------------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh.eeeeeeeee......hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eee............hhhhhhhhhhhhh.eee......hhhhhhhhhhhheeeee..-----...hhhhhhhhhhhh..hhhhh......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k32 F   3 LmDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADmIIEHKYPGPAIQYVHKTVLEILADEYSILADGTRRDDRVPKLSYSEIQSLEmRKNIQYITPLmGFGYKTLRHLASEFFILEEIK-----SSDYEAEIRHILKERGESPEKYFPEHKQTRVVGLKKEI 200
                             |      12        22        32        42        52        62        72|       82        92       102       112       122  |    132   |   142       152    |    -|      172       182       192        
                             4-MSE                                                               73-MSE                                             125-MSE    136-MSE              157   163
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K32)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3K32)

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  3k32
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  Y690_METJA | Q58102
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